ArticleGenome research2011
Transcriptome dynamics through alternative polyadenylation in developmental and environmental responses in plants revealed by deep sequencing.
Article in Genome research, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 49 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
49 citing papers in PubMed.
- Alternative Polyadenylation Dynamics During the Rice Blast Immune Response.Molecular plant pathology · 2026Article
- Stress responses of plants through transcriptome plasticity by mRNA alternative polyadenylation.Molecular horticulture · 2023Review
- A Global Survey of the Full-Length Transcriptome ofInternational journal of molecular sciences · 2023Article
- Natural variation in the plant polyadenylation complex.Frontiers in plant science · 2023Article
- NBBt-test: a versatile method for differential analysis of multiple types of RNA-seq data.Scientific reports · 2022Article
- Full-length transcriptome reconstruction reveals genetic differences in hybrids of Oryza sativa and Oryza punctata with different ploidy and genome compositions.BMC plant biology · 2022Article
- Improved Reference Genome Annotation ofFrontiers in plant science · 2022Article
- RNA architecture influences plant biology.Journal of experimental botany · 2021Review
- Alternative Polyadenylation in response to temperature stress contributes to gene regulation in Populus trichocarpa.BMC genomics · 2021Article
- A Tissue-Specific Landscape of Alternative Polyadenylation, lncRNAs, TFs, and Gene Co-expression Networks inFrontiers in plant science · 2021Article
- Full-Length Transcriptome Analysis ofFrontiers in cellular and infection microbiology · 2021Article
- PlantAPAdb: A Comprehensive Database for Alternative Polyadenylation Sites in Plants.Plant physiology · 2020Article
- Transcription Terminator-Mediated Enhancement in Transgene Expression in Maize: Preponderance of the AUGAAU Motif Overlapping With Poly(A) Signals.Frontiers in plant science · 2020Article
- Profiling Alternative 3' Untranslated Regions in Sorghum using RNA-seq Data.Frontiers in genetics · 2020Article
- Analysis of Alternative Splicing and Alternative Polyadenylation inFrontiers in genetics · 2020Article
- Genome-Wide Profiling of Polyadenylation Events in Maize Using High-Throughput Transcriptomic Sequences.G3 (Bethesda, Md.) · 2019Article
- Abiotic and biotic stresses induce a core transcriptome response in rice.Scientific reports · 2019Article
- SMRT sequencing analysis reveals the full-length transcripts and alternative splicing patterns inPeerJ · 2019Article
- Characterization of Full-Length Transcriptome Sequences and Splice Variants ofFrontiers in genetics · 2019Article
- Reviving the Transcriptome Studies: An Insight Into the Emergence of Single-Molecule Transcriptome Sequencing.Frontiers in genetics · 2019Review
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
10 authors.
Funding
Abstract
Polyadenylation sites mark the ends of mRNA transcripts. Alternative polyadenylation (APA) may alter sequence elements and/or the coding capacity of transcripts, a mechanism that has been demonstrated to regulate gene expression and transcriptome diversity. To study the role of APA in transcriptome dynamics, we analyzed a large-scale data set of RNA "tags" that signify poly(A) sites and expression levels of mRNA. These tags were derived from a wide range of tissues and developmental stages that were mutated or exposed to environmental treatments, and generated using digital gene expression (DGE)-based protocols of the massively parallel signature sequencing (MPSS-DGE) and the Illumina sequencing-by-synthesis (SBS-DGE) sequencing platforms. The data offer a global view of APA and how it contributes to transcriptome dynamics. Upon analysis of these data, we found that ∼60% of Arabidopsis genes have multiple poly(A) sites. Likewise, ∼47% and 82% of rice genes use APA, supported by MPSS-DGE and SBS-DGE tags, respectively. In both species, ∼49%-66% of APA events were mapped upstream of annotated stop codons. Interestingly, 10% of the transcriptomes are made up of APA transcripts that are differentially distributed among developmental stages and in tissues responding to environmental stresses, providing an additional level of transcriptome dynamics. Examples of pollen-specific APA switching and salicylic acid treatment-specific APA clearly demonstrated such dynamics. The significance of these APAs is more evident in the 3034 genes that have conserved APA events between rice and Arabidopsis.
Indexed as
Identifiers
What OpenQuestion holds
Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.